{"id":1996,"date":"2017-01-18T10:23:51","date_gmt":"2017-01-18T18:23:51","guid":{"rendered":"http:\/\/www.wou.edu\/chemistry\/?page_id=1996"},"modified":"2017-04-17T11:36:47","modified_gmt":"2017-04-17T18:36:47","slug":"ch105-chapter-5-organic-chemistry","status":"publish","type":"page","link":"https:\/\/wou.edu\/chemistry\/courses\/online-chemistry-textbooks\/ch105-consumer-chemistry\/ch105-chapter-5-organic-chemistry\/","title":{"rendered":"CH105: Chapter 5 – Introduction to Organic Chemistry"},"content":{"rendered":"

Chapter 5 \u2013 Introduction to Organic Chemistry<\/span><\/strong><\/h2>\n

This content can also be downloaded as Interactive PDF<\/a>. For the interactive PDF,<\/span> adobe reader <\/a><\/span>is required for full functionality.<\/span><\/span><\/p>\n

This text is published under creative commons licensing, for referencing and adaptation, please click<\/span> here. <\/em><\/strong><\/a><\/span><\/p>\n

Sections:<\/strong><\/span><\/h2>\n

5.1 <\/b>Pain, pleasure, and organic chemistry<\/strong><\/span><\/a><\/h3>\n

5.2 Drawing organic molecules<\/strong><\/span><\/span><\/b><\/a><\/h3>\n

Finding the Best Lewis Structure<\/strong><\/span><\/a><\/h4>\n

5.3 Different Representations of Organic Molecules<\/a>\u00a0<\/b><\/h3>\n

Molecular formulae<\/strong><\/span><\/a><\/h4>\n

Structural formulae and 3-dimensional models<\/strong><\/span><\/a><\/h4>\n

Skeletal or line formulae<\/strong><\/span><\/a><\/h4>\n

Drawing abbreviated organic structure<\/span><\/strong><\/a><\/h4>\n

5.4<\/b> Stereoisomers, Enantiomers, and Chirality<\/b><\/a><\/h3>\n

Chirality<\/strong><\/span><\/a><\/h4>\n

Thalidomide – A Story of Unintended Consequences<\/strong><\/span><\/a><\/h4>\n

5.5 The Importance of Chirality in Protein Interactions<\/strong><\/span><\/a>\u00a0<\/b><\/h3>\n

5.6 Recognizing Common Organic Functional Groups<\/b><\/a><\/h3>\n

Alkanes<\/strong><\/span><\/a><\/h4>\n

Alkenes and Alkynes<\/strong><\/span><\/a><\/h4>\n

Aromatics<\/strong><\/span><\/a><\/h4>\n

Alkyl Halides<\/strong><\/span><\/a><\/h4>\n

Alcohols, Phenols, and Thiols<\/strong><\/span><\/a><\/h4>\n

Ethers and Sulfides<\/strong><\/span><\/a><\/h4>\n

Amines<\/span><\/strong><\/a><\/h4>\n

Organic Phosphates<\/span><\/strong><\/a><\/h4>\n

Aldehydes and Ketones<\/span><\/strong><\/a><\/h4>\n

Carboxylic Acids and Their Derivatives<\/span><\/strong><\/a><\/h4>\n

Nitriles<\/span><\/strong><\/a><\/h4>\n

Practice Recognizing Functional Groups in Molecules<\/span><\/strong><\/a><\/h4>\n

5.7 A Brief Overview of Organic Nomenclature<\/b><\/a><\/h3>\n

5.8 References<\/span><\/strong><\/a><\/h3>\n
\n

5.1 <\/strong>Pain, pleasure, and organic chemistry<\/b><\/span><\/h3>\n

\"\"<\/a><\/p>\n

Habanero peppers <\/span>(credit:<\/span> https:\/\/www.flickr.com\/photos\/jeffreyww\/<\/span><\/a><\/span>)<\/span><\/p>\n

It’s a hot August evening at a park in the middle of North Hudson, Wisconsin, a village of just under 4000 people on the St. Croix river in the western edge of the state.\u00a0 A line of people are seated at tables set up inside a canvas tent.\u00a0 In front of a cheering crowd of friends, family, and neighbors, these brave souls are about to do battle . . .with a fruit plate.<\/p>\n

Unfortunately for the contestants, the fruit in question is the habanero, one of the hotter varieties of chili pepper commonly found in markets in North America.\u00a0 In this particular event, teams of five people will race to be the first to eat a full pound of peppers.\u00a0 As the eating begins, all seems well at first.\u00a0 Within thirty seconds, though, what begins to happen is completely predictable and understandable to anyone who has ever mistakenly poured a little too much hot sauce on the dinner plate.<\/p>\n

Faces turn red, sweat and tears begin to flow, and a copious amount of cold water is gulped down<\/span><\/a>.<\/span><\/p>\n

Although technically the contestants are competing against each other, the real opponent in this contest – the cause of all the pain and suffering –\u00a0 is the chemical compound ‘capsaicin’, the source of the heat in hot chili peppers.<\/p>\n

\"\"<\/a><\/p>\n

Composed of the four elements carbon, hydrogen, oxygen and nitrogen, capsaicin is produced by the pepper plant for the purpose of warding off hungry mammals.\u00a0 The molecule binds to and activates a mammalian receptor protein called TrpV1, which in normal circumstances has the job of detecting high temperatures and sending a signal to the brain – ‘it’s hot, stay away!’ \u00a0This strategy works quite well on all mammalian species except one: we humans (some of us, at least) appear to be alone in our tendency to actually seek out the burn of the hot pepper in our food.<\/p>\n

Interestingly, birds also have a heat receptor protein which is very similar to the TrpV1 receptor in mammals, but birds are not at all sensitive to capsaicin.\u00a0 There is an evolutionary logic to this: it is to the pepper’s advantage to be eaten by a bird rather than a mammal, because a bird can spread the pepper seeds over a much wider area.\u00a0 The region of the receptor which is responsible for capsaicin sensitivity appears to be quite specific. In 2002, scientists were able to insert a small segment of the (capsaicin-sensitive) rat TrpV1 receptor gene into the non-sensitive chicken version of the gene, and the resulting chimeric (mixed species) receptor was sensitive to capsaicin (Cell<\/span><\/em> <\/span>2002<\/span><\/strong>, <\/span>108<\/span><\/em>, 421<\/span><\/a><\/span>).<\/p>\n

Back at the North Hudson Pepperfest, those with a little more common sense are foregoing the painful effects of capsaicin overload and are instead indulging in more pleasant chemical phenomena. A little girl enjoying an ice cream cone is responding in part to the chemical action of another organic compound called vanillin.<\/p>\n

\"\"<\/a><\/p>\n

What is it about capsaicin and vanillin that causes these two compounds to have such dramatically different effects on our sensory perceptions? Both are produced by plants, and both are composed of the elements carbon, hydrogen, oxygen, and (in the case of capsaicin) nitrogen. Since the birth of chemistry as a science, chemists have been fascinated – and for much of that history, mystified – by the myriad properties of compounds that come from living things. The term ‘organic’, from the Greek organikos<\/em>, was applied to these compounds, and it was thought that they contained some kind of ‘vital force’ which set them apart from ‘inorganic’ compounds such as minerals, salts, and metals,\u00a0and which allowed them to operate by a completely different set of chemical principles.\u00a0 How else but through the action of a ‘vital force’ could such a small subgroup of the elements combine to form compounds with so many different properties?<\/p>\n

Today, as you are probably already aware, the term ‘organic,’ – when applied to chemistry – refers not just to molecules from living things, but to all compounds containing the element carbon, regardless of origin. Beginning early in the 19th century, as chemists learned through careful experimentation about the composition and properties of ‘organic’ compounds such as fatty acids, acetic acid and urea, and even figured out how to synthesize some of them starting with exclusively ‘inorganic’ components, they began to realize that the ‘vital force’ concept was not valid, and that the properties of both organic and inorganic molecules could in fact be understood using the same fundamental chemical principles.<\/p>\n

They also began to more fully appreciate the unique features of the element carbon which makes it so central to the chemistry of living things, to the extent that it warrants its own subfield of chemistry. Carbon forms four stable bonds, either to other carbon atoms or to hydrogen, oxygen, nitrogen, sulfur, phosphorus, or a halogen.\u00a0 The characteristic bonding modes of carbon allow it to serve as a skeleton, or framework, for building large, complex molecules that incorporate chains, branches and ring structures.<\/p>\n

Although ‘organic chemistry’ no longer means exclusively the study of compounds from living things, it is nonetheless the desire to understand and influence the chemistry of life that drives much of the work of organic chemists, whether the goal is to learn something fundamentally new about the reactivity of a carbon-oxygen bond, to discover a new laboratory method that could be used to synthesize a life-saving drug, or to better understand the intricate chemical dance that goes on in the active site of an enzyme or receptor protein. Although humans have been eating hot peppers and vanilla-flavored foods for centuries, we are just now, in the past few decades, beginning to understand how and why one causes searing pain and the other pure gustatory pleasure.\u00a0 We understand that the precise geometric arrangement of the four elements in capsaicin allows it to fit inside the binding pocket of the TrpVI heat receptor, but as of today, we do not yet have a detailed three dimensional picture of the TrpVI protein bound to capsaicin.\u00a0 We also know that the different arrangement of carbon, hydrogen and oxygen atoms in vanillin allows it to bind to specific olfactory receptors, but again, there is much yet to be discovered about exactly how this happens.<\/p>\n

In this chapter, you will be introduced to some of the most fundamental principles of organic chemistry.\u00a0 With the concepts we learn about, we can begin to understand how carbon and a very small number of other elements in the periodic table can combine in predictable ways to produce a virtually limitless chemical repertoire.<\/p>\n

As you read through, you will recognize that the chapter contains a lot of review of topics you have probably learned already in an introductory chemistry course, but there will likely also be a few concepts that are new to you, as well as some topics which are already familiar to you but covered at a greater depth and with more of an emphasis on biologically relevant organic compounds.<\/p>\n

We will begin with a reminder of how chemists depict bonding in organic molecules with the ‘Lewis structure’ drawing convention, focusing on the concept of ‘formal charge’. We will review the common bonding patterns of the six elements necessary for all forms of life on earth – carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus – plus the halogens (fluorine, chlorine, bromine, and iodine).\u00a0 We’ll then continue on with some of the basic skills involved in drawing and talking about organic molecules: understanding the ‘line structure’ drawing convention and other useful ways to abbreviate and simplify structural drawings, learning about functional groups and isomers, and looking at how to systematically name simple organic molecules.\u00a0 Finally, we’ll bring it all together with a review of the structures of the most important classes of biological molecules – lipids, carbohydrates, proteins, and nucleic acids – which we will be referring to constantly throughout the rest of the book.<\/p>\n

(<\/strong><\/em><\/span>Back to the Top<\/strong><\/em><\/span>)<\/strong><\/em><\/span><\/a><\/p>\n

\n

5.2 Drawing organic molecules<\/strong><\/span><\/h3>\n

 <\/p>\n

As\u00a0observed in the molecules capsaicin and vanillin above, the most common atoms\u00a0found in organic\u00a0compounds are carbon and hydrogen.\u00a0 Other atoms that routinely form covalent bonds within organic structures\u00a0also include\u00a0oxygen, nitrogen, sulfur and phosphorus.\u00a0 More rarely, halogens such as chlorine, bromine and iodine can also be incorporated into organic molecules.\u00a0 Recall from chapter 4, that the octet rule helped us determine that carbon routinely makes four covalent bonds, nitrogen and phosphorus each make three, oxygen\u00a0and sulfur each make two, and\u00a0the halogens only make one bond.\u00a0Hydrogen is an exception to the octet rule as it is the smallest element and its valence shell is filled with two electrons.\u00a0 Thus, hydrogen can form one bond with another atom. Sulfur and phosphorus can also have bonding patterns that are exceptions to the octet rule.\u00a0 They both have expanded orbital bonding with phosphorus also routinely forming five covalent bonds, and sulfur being capable of forming either four or six covalent bonds. Table 5.1 provides a graphic representation of these patterns. When you are drawing organic molecules, it is important to pay attention to the bonding rules so that all atoms reach their preferred bonding states.<\/p>\n

Table 5.1:\u00a0 Covalent Bonding Patterns of Atoms Commonly Found in Organic Molecules<\/span><\/strong><\/p>\n

\"\"<\/a><\/a><\/p>\n

*Note: Hydrogen doesn’t really follow the octet rule as its valence shell is full with 2 e–<\/sup><\/em><\/p>\n

 <\/p>\n

Finding the Best Lewis Structure<\/strong><\/span><\/h4>\n

 <\/p>\n

As we move forward in our study of organic molecules, we find that they become much more complex than the simple\u00a0ionic and covalent compounds discussed in Chapter 3. Because of this complexity, organic\u00a0compounds often have more than one specific structural state that they can exist in, and it is not uncommon\u00a0that a molecule might shift back and forth between these states.\u00a0 When electrons in a molecule can shift from one area of the molecule to another to create these alternative structures. This is\u00a0defined as resonance,<\/strong><\/em> and the\u00a0resulting states from these shifts as resonance structures<\/strong><\/em>.\u00a0Note that resonance structures give chemists a more concrete way of thinking about molecules.\u00a0 However, the actual molecules don’t exist in one structural state or another.\u00a0 Instead, they exist in a more amorphous transitional state that is somewhere in between all of the possible combinations. Certain resonance forms can be more stable than others and will\u00a0have more influence on\u00a0the overall structure of the molecule than other resonance forms.\u00a0 Thus, we need a way to accurately predict what resonance structures are likely to occur within a molecule, and which\u00a0states will be the most stable.\u00a0 This can be done using the formal charge method<\/em><\/strong> of drawing Lewis structures. The formal charge<\/strong><\/em> on an atom is calculated as the number of valence electrons of an atom minus the number of electrons an atom ‘owns’. The number of electrons owned by an atom can be calculated by\u00a0adding the number of unshared electrons + half of the number of shared electrons.\u00a0Remember that 2e<\/em>–<\/sup> are shared for every line drawn between two atoms (one line = 2e<\/em>–<\/sup>).\u00a0For example, if oxygen is bonded to two other atoms, we would calculate formal charge on the oxygen by subtracting the number of electrons \u2018owned\u2019 by the oxygen from its valence shell number of electrons:<\/p>\n

\"\"<\/a><\/a><\/p>\n

What if oxygen is bonded like this?<\/p>\n

\"\"<\/a><\/p>\n

How would you calculate the formal charge?<\/p>\n

\"\"<\/a><\/p>\n

This is not the preferred configuration for oxygen, but because oxygen is so electronegative, it can carry a negative formal charge more easily than atoms with less electronegativity.<\/p>\n

Now let’s consider the structure of the phosphate anion (PO4<\/sub>3-\u00a0<\/sup>).\u00a0 This is the most common form of phosphorus found in all living organisms on the planet, including humans. It is commonly incorporated into organic molecules such as DNA, proteins, and ATP (Adenosine Triphosphate), the energy storehouse of the cell (Figure 5.1).<\/p>\n

\"\"<\/a><\/p>\n

Figure 5.1 Structures of Adenosine Triphosphate (ATP) and Deoxyribonucleic Acid (DNA).<\/strong>\u00a0 The phosphate ion\u00a0is an important component of\u00a0both the (A.) ATP structure and the (B.) DNA structure.<\/p>\n

Diagram of DNA model provided by: Zephyris – Own work, CC BY-SA 3.0, https:\/\/commons.wikimedia.org\/w\/index.php?curid=15027555<\/p>\n

How do we go about drawing the Lewis Structure for the phosphate ion?<\/p>\n

(1) Identify the least electronegative element(s) in the molecule. This will be the central atom(s) that the other, more electronegative atoms, are bonded around. (Note that hydrogen can never be a central atom as it can only make one covalent bond).<\/p>\n